DOCSLIB.ORG

Revisiting the Landscape of Evolutionary Breakpoints Across Human Genome Using Multi-Way Comparison

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Revisiting the Landscape of Evolutionary Breakpoints Across Human Genome Using Multi-Way Comparison bioRxiv preprint doi: https://doi.org/10.1101/696245; this version posted July 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Revisiting the landscape of evolutionary breakpoints across human genome using multi-way comparison Golrokh Vitae1, Amine M. Remita1, Abdoulaye Banir´eDiallo1, 1 Universit´edu Qu´ebec A` Montr´eal * [email protected] Abstract Genome rearrangement is one of the major forces driving the processes of the evolution and disease development. The chromosomal position affected by these rearrangements are called breakpoints. The breakpoints occurring during the evolution of species are known to be non randomly distributed. Detecting their landscape and mapping them to genomic features constitute an important features in both comparative and functional genomics. Several studies have attempted to provide such mapping based on pairwise comparison of genes as conservation anchors. With the availability of more accurate multi-way alignments, we design an approach to identify synteny blocks and evolutionary breakpoints based on UCSC 45-way conservation sequence alignments with 12 selected species. The multi-way designed approach with the mild flexibility of presence of selected species, helped to have a better determination of human lineage-specific evolutionary breakpoints. We identified 261,391 human lineage-specific evolutionary breakpoints across the genome and 2,564 dense regions enriched with biological processes involved in adaptive traits such as response to DNA damage stimulus, cellular response to stress and metabolic process. Moreover, we found 230 regions refractory to evolutionary breakpoints that carry genes associated with crucial developmental process such as organ morphogenesis, skeletal system development, chordate embryonic development, nerve development and regulation of biological process. This initial map of the human genome will help to gain better insight into several studies including developmental studies and cancer rearrangement processes. Introduction 1 Genome rearrangement is one of the major forces driving the process of evolution, 2 population diversity and development of diseases including cancers. It happens when 3 DNA breaks in specific positions (breakpoints) and reassembles in a way different from 4 the initial genome conformation and changes the genome landscape [6]. It is now 5 well-accepted that genome rearrangements do not happen randomly along the genome 6 and not all genomic regions are susceptible to such dramatic modifications 7 [7, 25, 35, 36]. Millions of years of evolution and natural selection driven by these 8 structural modifications curved the genome in a way that regions carrying high 9 functional pressure maintained their integrity and could be identified as orthologs with 10 same order and on the same chromosome in a range of relatively close species. Hence, 11 resistance of genomic regions to any major modification implies that these regions 12 harbor functional importance to survival as well as reproduction of species and any 13 modification could have a deleterious effect in the process of natural selection [30]. 14 1/19 bioRxiv preprint doi: https://doi.org/10.1101/696245; this version posted July 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Studies on the genome synteny have shown that conserved regions are not only 15 significantly enriched in putative regulatory regions [23, 31] but also are associated with 16 transcriptional regulations and developmental processes [31, 41, 46]. On the other hand, 17 are the regions that are more receptive to rearrangements, participating in speciation, 18 adaptation and development of species-specific traits and behavior that are not 19 detrimental to the survival nor reproduction of the species. These break-prone regions 20 or "breakpoint hotspots" are also known to carry distinctive functional and structural 21 markers [10]. The identification of such regions are difficult and controversial due to 22 several assumptions. "Comparative genomics relies on the structuring of genomes into 23 syntenic blocks" [19]. However, comparative studies still lack a clear definition of 24 synteny. Since the term "synteny" was introduced, even the criteria that define the 25 synteny conservation vary from one study to another. Also, in most of the methods, to 26 identify synteny, synteny fragments were defined as a set of genes with a conserved 27 order [9, 37, 38, 40]. These issues are well discussed by Ghiurcuta, 2014 [19]. The lack 28 of clear definition, choice of granularity of study (minimum size), and different type of 29 comparison could led to have the high probability of different results generated by same 30 data [19]. One conclusion provided to tackle the drawback of these methods are to use 31 multi sets of homologous markers instead of only genes as anchors as well as extending 32 the pairwise comparison to multi-ways [19]. Moreover, the identification of synteny 33 breaks is affected by the selection of species. This influences the size and position of 34 synteny blocks and their corresponding breakpoints as breakpoint is not a tangible 35 physical entity in a genome; it is a result of an analytical construct based on the 36 comparison of selected genomes [42]. Other than exogenous factors, some biological 37 mechanisms such as non-allelic homologous recombination (NAHR) and non-homologous 38 endjoining (NHEJ) [20] and the presence of endogenous factors such as CpG islands [10], 39 GC content[13], some repeat elements [21, 24] and G-quadruplex [10, 39] could affect 40 the susceptibility of genomic regions to rearrangements. Due to some of these factors, 41 DNA could undergo a conformation change (e.g. from B to Z) that could destabilize the 42 molecule and make it prone to structural damage [2, 44, 47]. Also, phenomena such as 43 segmental duplications (SDs) [1, 3, 32], known to be associated evolutionary 44 breakpoints causing a double strand breaks on DNA structure. Hence, it is important to 45 revisit Evolutionary Breakpoints (EBrs) with more accurate and well-drafted 46 mammalian sequenced genomes and updated genomics features. In this paper we 47 propose a new map of accurate and more precise evolutionary breakpoints region based 48 on human lineage synteny breaks, multi-way comparison and ancestral breakpoint 49 reconstruction. Furthermore, we explore the hotspots of EBrs (EBHRs) based on their 50 coassociation to multiple structural and functional human genome features. 51 Results 52 0.1 Identification of human lineage-specific synteny breaks 53 Synteny block is a cluster of (relatively close) markers conserved among related genomes 54 that maintained their orientation and order. The regions bordered by synteny blocks 55 are the position of the genome that have been subjected to rearrangement in one or 56 more compared species since a common ancestor. Multi-way comparative analysis of 57 human genome with 10 other mammals and chicken (see supplementary table S2), 58 revealed 261,420 synteny blocks covering 52% of the human genome with a size 59 distribution from 1 Kbp to 200 Kbp. The corresponding 261,391 genomic regions were 60 identified as human lineage-specific synteny breaks or evolutionary breakpoints (EBrs). 61 30 break regions were eliminated due to their size higher than 2 Mbp. These regions are 62 whether on centromeric or telomeric regions or on genomic regions with missing 63 2/19 bioRxiv preprint doi: https://doi.org/10.1101/696245; this version posted July 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Figure 1. Coverage of chromosomes by EBrs Figure 2. The percentages of human lineage specific breakpoints origin along the vertebrates reference tree information. See table 1. EBrs are associated with 39.58% of the human genome. 64 However, the coverage of breakpoints raise to over 40% in chr11, chr12, chr8, chr4 and 65 chr7 and to over 55% in chr19 and chrX. See figure 1. The size of these regions were 66 from 1 bp to 1.857 Mbp. The seven largest EBrs (size > 1 Mbp) were located chr14, 67 chrY, chr11, chrX, chr2 and chr7. Based on a Least Common Ancestor approach, we 68 identify the lineage-specific breakpoints, over 50% of these breakpoints were reused and 69 originated from separation of placental mammals. The next most representative 70 ancestral node was the Boreotherian ancestor with 20% of EBrs that originated from. 71 Others were originated from various ancestry nodes along the reference phylogeny tree 72 with a representation between < 1% to about 10%. The distribution of EBr ancestry 73 origins are presented in figure 2. 74 Method Input Output Size of output Conservation anchor extraction 45-way multiple alignments Conservation anchors 21,809,215 Fusion Conservation anchors Synteny clusters 346,515 filter according to length Synteny clusters Synteny blocks 261,420 Synteny break extraction Synteny blocks Synteny breaks 261,421 Size filter Synteny breaks EBrs 261,391 Permutation EBrs EBHRs 2,564 EBr desert extraction EBrs + human genome EBRRs 230 Table 1. Summary of EBr-related results 3/19 bioRxiv preprint doi: https://doi.org/10.1101/696245; this version posted July 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 0.2 Localisation of breakpoint hotspots 75 Using an overlapping sliding window approach of 100 Kbp and a permutation test with 76 100,000 iterations, we identified 2,564 regions as EBr hotspot regions (EBHRs). 77 Although evolutionary breakpoints are distributed across 90% of genomic windows, only 78 8.28% of genomic windows (2,564) were enriched in EBrs (p-value < 0.05). The results 79 show that EBHRs contain 12 to 21 EBrs with an average of 14:85 ± 1:56 (except 80 chromosome Y).
Load more

Recommended publications
  • Constraints on Genes Shape Long-Term Conservation of Macro-Synteny in Metazoan Genomes
    Lv et al. BMC Bioinformatics 2011, 12(Suppl 9):S11 http://www.biomedcentral.com/1471-2105/12/S9/S11 PROCEEDINGS Open Access Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes Jie Lv, Paul Havlak, Nicholas H Putnam* From Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Com- parative Genomics Galway, Ireland. 8-10 October 2011 Abstract Background: Many metazoan genomes conserve chromosome-scale gene linkage relationships (“macro-synteny”) from the common ancestor of multicellular animal life [1-4], but the biological explanation for this conservation is still unknown. Double cut and join (DCJ) is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis [5], but as we show here, it is not sufficent to explain long-term macro- synteny conservation. Results: We examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context (“DCJ-[C]”), and is available as open source software from http://github.com/ putnamlab/dcj-c. Conclusions: A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro- synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.
    [Show full text]
  • About Synteny Analysis
    Chris Shaffer Last update: 08/11/2021 About Synteny Analysis In eukaryotes, synteny analysis is really the investigation of how chromosomes, or large sections of chromosomes evolve over time. To investigate this, scientists compare the order and orientation of either genes or DNA sequences between homologous chromosomes from two or more species (syntenic blocks). Genes within a syntenic region may have similar functional constraints or regulatory regimes that function best when they are kept together. In the lab, flies exhibit chromosomal changes such as duplications, deletions, and inversions, particularly when exposed to mutagens such as x-rays; the question is what kinds of changes happen in the wild, and at what rate? Analysis of such changes gives us information about what changes can be tolerated and provides insights into speciation. To search for chromosome changes that occurred over the course of fruit fly evolution, you can compare the order and orientation of the genes in your project with the order and orientation of the orthologous genes in Drosophila melanogaster. There are three basic steps to the process: 1. Determine orthologs If you are going to decide how genes change order/orientation you first need to make sure you are looking at orthologous genes in each species. If you have assigned orthology during annotation you can use that assignment. If not, you will need to do cross-species BLAST searches. 2. Assess position Once you have the orthology assigned, use your favorite genome browser (e.g. GBrowse or JBrowse on FlyBase) to find the position and orientation of each gene in your project.
    [Show full text]
  • “Parent-Daughter” Relationships Among Vertebrate Paralogs
    Reconstruction of the deep history of “Parent-Daughter” relationships among vertebrate paralogs Haiming Tang*, Angela Wilkins Mercury Data Science, Houston, TX, 77098 * Corresponding author Abstract: Gene duplication is a major mechanism through which new genetic material is generated. Although numerous methods have been developed to differentiate the ortholog and paralogs, very few differentiate the “Parent-Daughter” relationship among paralogous pairs. As coined by the Mira et al, we refer the “Parent” copy as the paralogous copy that stays at the original genomic position of the “original copy” before the duplication event, while the “Daughter” copy occupies a new genomic locus. Here we present a novel method which combines the phylogenetic reconstruction of duplications at different evolutionary periods and the synteny evidence collected from the preserved homologous gene orders. We reconstructed for the first time a deep evolutionary history of “Parent-Daughter” relationships among genes that were descendants from 2 rounds of whole genome duplications (2R WGDs) at early vertebrates and were further duplicated in later ceancestors like early Mammalia and early Primates. Our analysis reveals that the “Parent” copy has significantly fewer accumulated mutations compared with the “Daughter” copy since their divergence after the duplication event. More strikingly, we found that the “Parent” copy in a duplication event continues to be the “Parent” of the younger successive duplication events which lead to “grand-daughters”. Data availability: we have made the “Parent-Daughter” relationships publicly available at https://github.com/haimingt/Parent-Daughter-In-Paralogs/ Introduction Gene duplication has been widely accepted as a shaping force in evolution (Zhang, et al.
    [Show full text]
  • Calcisponges Have a Parahox Gene and Dynamic Expression of 2 Dispersed NK Homeobox Genes 3
    1 Calcisponges have a ParaHox gene and dynamic expression of 2 dispersed NK homeobox genes 3 4 Sofia A.V. Fortunato1, 2, Marcin Adamski1, Olivia Mendivil Ramos3, †, Sven Leininger1, , 5 Jing Liu1, David E.K. Ferrier3 and Maja Adamska1§ 6 1Sars International Centre for Marine Molecular Biology, University of Bergen, 7 Thormøhlensgate 55, 5008 Bergen, Norway 8 2Department of Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, 9 Norway 10 3 The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of 11 St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK. 12 † Current address: Stanley Institute for Cognitive Genomics, Cold Spring Harbor 13 Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. 14 Current address: Institute of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway 15 §Corresponding author 16 Email address: [email protected] 17 18 Summary 19 Sponges are simple animals with few cell types, but their genomes paradoxically 20 contain a wide variety of developmental transcription factors1‐4, including 21 homeobox genes belonging to the Antennapedia (ANTP)class5,6, which in 22 bilaterians encompass Hox, ParaHox and NK genes. In the genome of the 23 demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, 24 but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians5. 25 It has been proposed that Hox and ParaHox genes originated from NK cluster 26 genes after divergence of sponges from the lineage leading to cnidarians and 27 bilaterians5,7. On the other hand, synteny analysis gives support to the notion that 28 absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss 29 (the ghost locus hypothesis)8.
    [Show full text]
  • Breakup of a Homeobox Cluster After Genome Duplication in Teleosts
    Breakup of a homeobox cluster after genome duplication in teleosts John F. Mulley*, Chi-hua Chiu†, and Peter W. H. Holland*‡ *Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom; and †Rutgers University, Department of Genetics, Life Sciences Building, Piscataway, NJ 08854 Edited by Eric H. Davidson, California Institute of Technology, Pasadena, CA, and approved May 11, 2006 (received for review January 13, 2006) Several families of homeobox genes are arranged in genomic been active throughout vertebrate history, we show that in the clusters in metazoan genomes, including the Hox, ParaHox, NK, ray-finned fish clade, the ParaHox gene cluster was lost in the Rhox, and Iroquois gene clusters. The selective pressures respon- evolution of teleosts after divergence from more basal ray- sible for maintenance of these gene clusters are poorly under- finned fish. stood. The ParaHox gene cluster is evolutionarily conserved be- tween amphioxus and human but is fragmented in teleost fishes. Results We show that two basal ray-finned fish, Polypterus and Amia, each We searched the emerging genome sequences of zebrafish possess an intact ParaHox cluster; this implies that the selective (Danio rerio; www.sanger.ac.uk͞Projects͞D࿝rerio) and two pressure maintaining clustering was lost after whole-genome pufferfish [Tetraodon nigroviridis (10) and Takifugu rubripes duplication in teleosts. Cluster breakup is because of gene loss, not (11)] for DNA sequences assignable to the Gsx, Xlox, and Cdx transposition or inversion, and the total number of ParaHox genes gene families. Comparison between species gave a consistent is the same in teleosts, human, mouse, and frog.
    [Show full text]
  • Inferring Synteny Between Genome Assemblies: a Systematic Evaluation Dang Liu1,2, Martin Hunt3,4 and Isheng J Tsai1,2*
    Liu et al. BMC Bioinformatics (2018) 19:26 DOI 10.1186/s12859-018-2026-4 RESEARCH ARTICLE Open Access Inferring synteny between genome assemblies: a systematic evaluation Dang Liu1,2, Martin Hunt3,4 and Isheng J Tsai1,2* Abstract Background: Genome assemblies across all domains of life are being produced routinely. Initial analysis of a new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. It is unknown to what extent draft assemblies lead to errors in such analysis. Results: We fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests raise questions about the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, assembly scaffolding using a reference guided approach with a closely related species may result in chimeric scaffolds with inflated assembly metrics if a true evolutionary relationship was overlooked. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous. Conclusions: Our results show that a minimum N50 of 1 Mb is required for robust downstream synteny analysis, which emphasizes the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.
    [Show full text]
  • A Fast, General Synteny Detection Engine
    bioRxiv preprint doi: https://doi.org/10.1101/2021.06.03.446950; this version posted June 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Discovery, Article A fast, general synteny detection engine Joseph B. Ahrens1*, Kristen J. Wade1 and David D. Pollock1* 1Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Denver, Colorado, USA * Corresponding authors Joseph B. Ahrens E-mail: [email protected] David D. Pollock E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.03.446950; this version posted June 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The increasingly widespread availability of genomic data has created a growing need for fast, sensitive and scalable comparative analysis methods. A key aspect of comparative genomic analysis is the study of synteny, co-localized gene clusters shared among genomes due to descent from common ancestors. Synteny can provide unique insight into the origin, function, and evolution of genome architectures, but methods to identify syntenic patterns in genomic datasets are often inflexible and slow, and use diverse definitions of what counts as likely synteny. Moreover, the reliable identification of putatively syntenic regions (i.e., whether they are truly indicative of homology) with different lengths and signal to noise ratios can be difficult to quantify.
    [Show full text]
  • Identifying Regions of Conserved Synteny Between
    IDENTIFYING REGIONS OF CONSERVED SYNTENY BETWEEN PEA (PISUM SPP.), LENTIL (LENS SPP.), AND BEAN (PHASEOLUS SPP.) by Matthew Durwin Moffet A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Plant Sciences MONTANA STATE UNIVERSITY Bozeman, Montana August 2006 © COPYRIGHT by Matthew Durwin Moffet 2006 All Rights Reserved ii APPROVAL of a thesis submitted by Matthew Durwin Moffet This thesis has been read by each member of the thesis committee and has been found to be satisfactory regarding content, English usage, format, citations, bibliographic style, and consistency, and is ready for submission to the Division of Graduate Education. Dr. Norman Weeden Approved for the Department of Plant Sciences and Plant Pathology Dr. John Sherwood Approved for the Division of Graduate Education Dr. Carl A. Fox iii STATEMENT OF PERMISSION TO USE In presenting this thesis in partial fulfillment of the requirements for a master’s degree at Montana State University, I agree that the Library shall make it available to borrowers under rules of the Library. If I have indicated my intention to copyright this thesis by including a copyright notice page, copying is allowable only for scholarly purposes, consistent with “fair use” as prescribed in the U.S. Copyright Law. Requests for permission for extended quotation from or reproduction of this thesis in whole or in parts may be granted only by the copyright holder. Matthew Durwin Moffet August 2006 iv ACKNOWLEDGEMENTS I would like to acknowledge and thank the following individuals: my past and present academic advisors Dr. Dan Bergey, Dr.
    [Show full text]
  • Comparative Physical Mapping Links Conservation of Microsynteny to Chromosome Structure and Recombination in Grasses
    Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses John E. Bowers*, Miguel A. Arias*, Rochelle Asher*, Jennifer A. Avise*, Robert T. Ball*, Gene A. Brewer*, Ryan W. Buss*, Amy H. Chen*, Thomas M. Edwards*, James C. Estill*, Heather E. Exum*, Valorie H. Goff*, Kristen L. Herrick*, Cassie L. James Steele*, Santhosh Karunakaran*, Gmerice K. Lafayette*, Cornelia Lemke*, Barry S. Marler*, Shelley L. Masters*, Joana M. McMillan*, Lisa K. Nelson*, Graham A. Newsome*, Chike C. Nwakanma*, Rosana N. Odeh*, Cynthia A. Phelps*, Elizabeth A. Rarick*, Carl J. Rogers*, Sean P. Ryan*, Keimun A. Slaughter*, Carol A. Soderlund†, Haibao Tang*, Rod A. Wing‡, and Andrew H. Paterson*§ *Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602; and †Arizona Genomics Computational Laboratory and ‡Arizona Genomics Institute, University of Arizona, Tucson, AZ 95721 Edited by Ronald L. Phillips, University of Minnesota, St. Paul, MN, and approved July 28, 2005 (received for review March 22, 2005) Nearly finished sequences for model organisms provide a founda- duplication in sorghum appears to be Ϸ70 mya (1) vs. Ϸ12 mya in tion from which to explore genomic diversity among other taxo- maize (4) and Ͻ5 mya in sugarcane (5), promising a higher success nomic groups. We explore genome-wide microsynteny patterns rate in relating sorghum genes to phenotypes by knockouts than between the rice sequence and two sorghum physical maps that either maize or sugarcane genes. Comparison of SB and closely integrate genetic markers, bacterial artificial chromosome (BAC) related Sorghum propinquum (SP) promises to shed new light on fingerprints, and BAC hybridization data.
    [Show full text]
  • Assembly and Validation of Conserved Long Non-Coding Rnas in the Ruminant
    bioRxiv preprint doi: https://doi.org/10.1101/253997; this version posted January 25, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Assembly and validation of conserved long non-coding RNAs in the ruminant 2 transcriptome 3 4 Stephen J. Bush1, 2, Charity Muriuki1, Mary E. B. McCulloch1, Iseabail L. Farquhar3, Emily 5 L. Clark1*, David A. Hume1, 4 * † 6 7 1 The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, 8 EH25 9RG 9 2 Experimental Medicine Division, Nuffield Department of Clinical Medicine, University of 10 Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU 11 3 Centre for Synthetic and Systems Biology, CH Waddington Building, Max Borne Crescent, 12 King’s Buildings, University of Edinburgh, EH9 3BF 13 4 Mater Research-University of Queensland, Translational Research Institute, 37 Kent Street, 14 Woolloongabba, Queensland 4102, Australia 15 * These authors contributed equally to this work. 16 † Corresponding author: [email protected] / [email protected] 17 18 Email addresses: 19 Stephen J. Bush [email protected] / [email protected] 20 Charity Muriuki [email protected] 21 Mary E. B. McCulloch [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/253997; this version posted January 25, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Multiple Roles of Secretory Lipocalins (Mup, Obp) in Mice
    Folia Zool. – 58 (Suppl. 1): 29–40 (2009) Multiple roles of secretory lipocalins (Mup, Obp) in mice Romana STOPKOVÁ1, Denisa HLADOVCOVÁ1, Juraj KOKAVEC2, Daniel VYORAL2 and Pavel STOPKA1,3* 1 Department of Zoology, Faculty of Science, Charles University, Prague, Viničná 7, Prague, 128 44, Czech Republic; e-mail: [email protected] 2 Pathological Physiology and Center of Experimental Hematology, First Faculty of Medicine, Charles University in Prague, Czech Republic 3 Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburska 89, 277 21 Libechov, Czech Republic Received 1 December 2008; Accepted 1 April 2009 Abstract. Many biological processes involve globular transport proteins belonging to a family called lipocalins. The prominent feature in lipocalin structure is their specific tertiary conformation forming eight-stranded beta barrel with capacity to bind various ligands inside. The importance of lipocalins is evident from the list of vital substances (hydrophobic ligands including vitamin A, steroids, bilins, lipids, pheromones etc.) that these proteins transport and from their high expression levels in various tissues. Among wide spectrum of lipocalins, Major Urinary Proteins (Mup) and Odorant Binding Proteins (Obp) are well known for their capacity to bind and carry odorants / pheromones and have been studied to detail in various mammalian models including mice, rats, and hamsters. However, many lipocalins (also including Mups) have previously been described with respect to their protective function in mammalian organism where they transport potentially harmful molecules to a degradation site (e.g. lysozomes) or straight out of the body. As most of lipocalins share similar tertiary structure, their potential role in both transport and excretion processes may be additive or complementary.
    [Show full text]
  • Whole-Genome Microsynteny-Based Phylogeny of Angiosperms Tao
    Whole-genome microsynteny-based phylogeny of angiosperms Tao Zhao ( [email protected] ) Ghent University Jiayu Xue Institute of Botany, Jiangsu Province and Chinese Academy of Sciences Arthur Zwaenepoel Ghent University Shu-min Kao Ghent University Zhen Li Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium. M. Schranz Wageningen University https://orcid.org/0000-0001-6777-6565 Yves Van de Peer Ghent University https://orcid.org/0000-0003-4327-3730 Article Keywords: Synteny network, gene order, matrix representation, phylogeny, angiosperms, maximum- likelihood Posted Date: August 17th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-51378/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License 1 Whole-genome microsynteny-based phylogeny of angiosperms 2 3 Tao Zhao1,2,3, Jia-Yu Xue4, Arthur Zwaenepoel1,2, Shu-Min Kao1,2, Zhen Li1,2, M. Eric 4 Schranz5, Yves Van de Peer1,2,6,7 5 6 1Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 7 Belgium. 8 2Center for Plant Systems Biology, VIB, Ghent, Belgium. 9 3State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory 10 of Apple, College of Horticulture, Northwest A & F University, Yangling, 712100, 11 China. 12 4Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 13 China. 14 5Biosystematics Group, Wageningen University and Research, Wageningen, The 15 Netherlands. 16 6Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics 17 and Microbiology, University of Pretoria, Pretoria, South Africa. 18 7College of Horticulture, Nanjing Agricultural University, Nanjing, China.
    [Show full text]